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1 <tool id="correlation_clustering" name="PathOGiST - Correlation Clustering" version="1.0.0">
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2 <description>: Runs correlation clustering on a distance matrix file</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.1">pathogist</requirement>
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5 </requirements>
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6
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7 <command><![CDATA[
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8 PATHOGIST correlation $constraints $distance $threshold cc.tsv
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9 ]]></command>
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10
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11 <inputs>
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12 <param name="distance" type="data" format="tabular,txt" label="Distance Matrix"/>
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13 <param name="threshold" type="integer" value="0" label="Threshold Value"
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14 help="The threshold value can be determined by visualizing the distance matrix"/>
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15 <param name="constraints" type="boolean" checked="false" truevalue="--all_constraints" falsevalue=""
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16 label="All Constraints"
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17 help="Add all constraints to the optimization problem, not just those with mixed signs"/>
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18 </inputs>
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19
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20 <outputs>
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21 <data name="clustering" label="Correlation clustering of ${on_string}" format="tabular" from_work_dir="cc.tsv"/>
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22 </outputs>
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23
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24 <help>
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25
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26 </help>
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27
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28 <citations>
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29
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30 </citations>
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31 </tool>
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